gmt music proximity

NAME

       gmt music proximity - Perform a proximity analysis on a list of mutations.

VERSION

       This document describes gmt music proximity version 0.04 (2016-01-01 at 23:10:19)

SYNOPSIS

       gmt music proximity --maf-file=? --output-file=? --output-dir=? [--max-proximity=?]
       [--skip-non-coding] [--skip-silent]

        ... music proximity \
               --maf-file input_dir/myMAF.tsv \
               --output-dir output_dir/ \
               --max-proximity 15

REQUIRED ARGUMENTS

       maf-file  Text
           List of mutations using TCGA MAF specifications v2.3

       output-file  Text
           TODO

       output-dir  Text
           Directory where output files will be written

OPTIONAL ARGUMENTS

       max-proximity  Text
           Maximum allowed AA distance between 2 mutations

           Default value '7' if not specified

       skip-non-coding  Boolean
           Skip non-coding mutations from the provided MAF file

           Default value 'true' if not specified

       noskip-non-coding  Boolean
           Make skip-non-coding 'false'

       skip-silent  Boolean
           Skip silent mutations from the provided MAF file

           Default value 'true' if not specified

       noskip-silent  Boolean
           Make skip-silent 'false'

DESCRIPTION

       This module first calculates the amino acid position of each mutation in the MAF file
       within its respective transcript. Then, for each mutation, two values are calculated: 1)
       the number of other mutations on the same transcript within the proximity limit set by the
       max-proximity input parameter, and 2) the distance to the closest other mutation in this
       nearby set. Only mutations which have another mutation within close proximity are reported
       in the output-file.

       In addition to the standard version 2.3 MAF headers, there needs to be 3 columns appended.
       These column headers in the MAF must have these names in the header in order for the tool
       to find them:
          transcript_name - the transcript name, such as NM_000028  amino_acid_change - the amino
       acid change, such as p.R290H
               c_position - the nucleotide position changed, such as c.869

       The output is generated with the folowing column headers: Mutations_Within_Proximity,
       Nearest_Mutation, Gene, Transcript, Affected_Amino_Acid(s), Chr, Start, Stop, Ref_Allele,
       Var_Allele, Sample

AUTHORS

        Nathan D. Dees, Ph.D.
        Dan Koboldt, M.S.
        Cyriac Kandoth, Ph.D.